The San Francisco Bunker had one guy station there and he wasn't even in power armor. The technology gap between the two groups isn't that immense and the brotherhood would have a lot more practical combat experence then the Enclave having been active in the wasteland instead of isolated on the oil rig. If the brotherhood managed to take out Navarro it cripple the Enclave's airforce as the base was needed for refueling Vertibirds from the Oil Rig.
Here's the problem with the Enclave(FO2) vs Brotherhood(FO2). The battle never could have been that limited. The Enclave chose the virus method because they didn't have the necessary resources to wage war over the mainland. The Brotherhood could also count on allies as at the time they were still friendly with the NCR. Which would end with the Enclave being forced to retreat to the Oil RIg.
I would say the tech gap is pretty huge. For one the Enclave can make power armour, T-51b, Advanced PA and APA MKII and the BoS can't. The Enlcave also had Vertibirds as well as well as plasma weapons and the BoS didn't.
The BoS could have counted NCR as allies but NCR but at the time of Fallout 2, NCR wasn't fully established in the North. The San Francisco bunker is proof the Enclave was actively taking out Brotherhood Bunkers. Since the BoS ask us to give them Vertibird blueprints, shows they were looking for a way to even the odds. The Enclave went with FEV plan because even with all their military power they were completely out numbered. NCR had 700,000 alone at that time. And the Enclave had what a 1000 people maybe a couple hundred more than that?
If all the BoS and all the Enclave of Fallout 2 met on some battlefield and had it out. Chances are the BoS would have a chance. Yet the Enclave can locate and fly to each buncker and pick them off. Not giving the BoS a chance to group in any sizeable force.